核酸序列数据库(genbank)和基因组数据库(ensemble)的区别

一、核酸序列数据库(genbank)和基因组数据库(ensemble)的区别

核酸序列数据库（genbank）和基因组数据库（ensemble）的区别：

1、GenBank是一个有来自于70,000多种生物的核苷酸序列的数据库。每条纪录都有编码区（CDS）特征的注释，还包括氨基酸的翻译。GenBank属于一个序列数据库的国际合作组织，包括EMBL和DDBJ。

2、Ensemble数据库可为药物研发提供超过167,000种生物活性化合物包括化学结构在内的必要信息。本数据库利用用户容易掌握的界面将数据、文本和图象资料有机地结合起来，便于查询。Ensemble可从药品专利开始，再通过其临床前和临床研究资料，直至注册信息、市场概况及其他方面的相关资料来跟踪药物。数据库每月更新一次，每年增加约10,000种新化合物。

二、解析Ensembl 的数据库服务器(图文详解)

1、在生物信息学的学习中，Ensembl是不可或缺的工具，我们通常通过网页访问它，如 uswest.ensembl.org/index.html，这个界面就像在线商店的展示，而其背后的数据存储则隐藏在数据库服务器中，对我们的研究至关重要。

2、Ensembl的数据仓库由四个服务器地址支撑，提供匿名访问权限，这使得我们在数据库层面的操作更为灵活，能够获取更详细的信息。Ensembl依赖 MySQL和 MariaDB这两大数据库管理系统，它们的起源和关系略有渊源：MySQL由麦克尔·维德纽斯开发，后被 Oracle收购，社区成员为避免版权风险，创立了 MariaDB。

3、要连接 Ensembl的数据库服务器，可以使用 Navicat工具，选择 MySQL连接，填写适当的服务器地址以优化访问速度。例如，连接到人类 hg38基因组的 Ensembl 104版本架构数据库，其名称遵循特定格式。

4、Ensemble的核心数据库，如 Core数据库，采用了星型、雪花型和星系型等多种维度模型来组织数据。星型模型是最基础的，由事实表和维度表构成，如基因信息表（gene）、等位基因表（alt_allele）和基因属性表（gene_attrib）。雪花型模型通过细分维度表，增加了信息维度，而星系型则涉及多个事实表共享维度表，Ensembl实际上采用了星系型来保证数据的全面性和清晰性。

5、对于生信分析师，理解这些模型有助于更高效地检索和利用 Ensembl数据。深入学习更多生信数据库知识，可以访问 zhenglei.blog.csdn.net获取更新内容。

三、请教关于intersystems 的cache数据库的相关知识

1、安装cache之前必须先安装IIS。//用来解析CSP

IIS在控制面板->添加或删除程序->添加/删除Windows组件->Internet信息服务(IIS)添加；

2、cache(Ensemble)安装步骤总共十二步;

4.拷贝原库Cache.cpf到EnsembleSys根目录下，cpf中主要配置数据库存放路径，根据事情情况可以自己修改cpf文件，或者在

System management Portal->Local Databases->Home->Configuration->Local Databases->Edit;

5.拷贝Cache.key到EnsembleSys\Mgr根目录下；

1、设置路径： [Home]> [Security Management]> [CSP Applications]> [Create NEW CSP Application]>[Save]；

2、Csp Application路径为IE访问路径

3、Resource required to run the application:%Service CSP;

4、Namespace:————————;

5、CachePhysicalPath:“数据库存放路径”

6、Default Superclass: locale.Chinese

设置路径[Home]> [Configuration]>[CSP Gateway Management]

Server Access（一般安装数据库后自动生成）

Application Access（需要添加一个）

IIS中虚拟目录设置//只使用数据库不考虑

操作路径：控制面板->管理工具->Internet信息服务->(本地计算机->网站->默认网站)。如果以前添加了站点，那么在完成上一步CSP设置之后，需要删除原来的IIS站点，重新添加。

2、第四步目录名称必须指向数据存放路径下，

3、第四步执行权限全选；//写CLS CSP需要配置

注意：在做补丁之前需要把CACHELIB的ReadOnly更改为No，做完补丁后再更改回Yes。

将以下内容拷贝到C:\EnsembleSys\Mgr\FDBMS

Patch\FDBMS_F173_Cache_52_WNT下CACHE.DAT文件

将以下内容拷贝到C:\EnsembleSys\CSP\sys\mgr

Patch\adhoc5412plus\adhoc5412\UtilConfigSQL.csp

FDBMS>d ^mdbmsins("","FDBMS")

Converting User Security Definitions.....DONE

Load routines from a%ROMF file.

WARNING: This routine will delete the source code(if any)

for existing object routines that are being replaced.

Device: C:\patch\FDBMS_F173_Cache_52_WNT\qarmacF173.mro

M/WNT wrote this file on Nov 03 2006 3:03 PM.

File Comment: patch for compiling routines in FDBMS

If a selected routine has the same name as one already on file,

shall it replace the one on file? No=> yes

Building existing routine list... done.

@ indicates routines which have been saved to disk.

. indicates routines which already exist in this directory.

1 routine in 0 minutes, 0 seconds

Load routines from a%ROMF file.

WARNING: This routine will delete the source code(if any)

for existing object routines that are being replaced.

Device: C:\patch\FDBMS_F173_Cache_52_WNT\SYS.SQLSRV.mro

M/WNT wrote this file on Nov 03 2006 3:03 PM.

File Comment: patch for compiling routines in FDBMS

If a selected routine has the same name as one already on file,

shall it replace the one on file? No=> yes

Building existing routine list... done.

@ indicates routines which have been saved to disk.

. indicates routines which already exist in this directory.

再做adhoc5412plus.zip（如文档readme_5412.txt，需要拷贝UtilConfigSQL.csp到C:\EnsembleSys\CSP\sys\mgr下）；

Input routines from Sequential

Device: C:\patch\adhoc5412plus\adhoc5412\adhoc5412.rsa

File written by Cache for Windows using%RO on 17 May 2007 9:32 PM

with extensions INC,INT and with description:

If a selected routine has the same name as one already on file,

shall it replace the one on file? No=> yes

Display Syntax Errors? Yes=> yes

^ indicates routines which will replace those now on file.

@ indicates routines which have been [re]compiled.

- indicates routines which have not been filed.

%msql.INC^ syConfig.INC^ STUCNFG1.INT@

%SYS>s path="C:\patch\adhoc5412plus\adhoc5412\SQL.xml"

%SYS>do$SYSTEM.OBJ.Load(path,"cbrps")

Load started on 04/12/2008 10:56:40

Loading file C:\patch\adhoc5412plus\adhoc5412\SQL.xml as xml

Compiling routine%SYSTEM.SQL.1

ERROR: Compiling class includes

Processing%systemInclude.INC into a precompiled header

%SYS>s path="C:\patch\adhoc5412plus\adhoc5412\adhoc5412.xml"

%SYS>do$SYSTEM.OBJ.Load(path,"brpsu")

Load started on 04/12/2008 10:57:57

Loading file C:\patch\adhoc5412plus\adhoc5412\adhoc5412.xml as xml

Imported object code:%SYS.PATCH

Imported global: ^CacheTempPatch

Default directory is c:\ensemblesys\mgr\

Created at: 2007-05-18 00:51:28

Created on$zv: Cache for Windows(Intel) 5.2.3(Build 710)

Please test the patch. If it fails, you can remove the

patch by executing the following command:

%SYS>d$System.CSP.LoadPage("/csp/sys/mgr/UtilConfigSQL.csp","fc")

Compiling file/csp/sys/mgr/UtilConfigSQL.csp

Compiling class%cspapp.mgr.utilconfigsql

Compiling routine%cspapp.mgr.utilconfigsql.1

%SYS>d$System.OBJ.Load("C:\patch\Collection.ListOfDT.xml","fc")

Load started on 04/12/2008 12:17:50

Loading file C:\patch\Collection.ListOfDT.xml as xml

Imported class:%Collection.ListOfDT

Compiling class%Collection.ListOfDT

Compiling routine%Collection.ListOfDT.1

Load routines from a%ROMF file.

WARNING: This routine will delete the source code(if any)

for existing object routines that are being replaced.

Device: C:\EnsembleSys\Mgr\FDBMS\qaqcasl523.mro

M/WNT wrote this file on May 18 2007 3:48 PM.

File Comment: backport of AK626, fix INTO:Array() problem

If a selected routine has the same name as one already on file,

shall it replace the one on file? No=> yes

Building existing routine list... done.

@ indicates routines which have been saved to disk.

. indicates routines which already exist in this directory.

1 routine in 0 minutes, 0 seconds

DHC-APP>d$system.SQL.Purge(0)

[Home]> [Configuration]> [SQL Settings]

将DISTINCT optimization turned on的值置为 Yes,保存,然后再置成No保存.

全部做完后把CACHELIB的ReadOnly更改为Yes